Configuration

Edit the file config.xml into the BiNS-Simulator folder and define all simulation parameters, such as the database connection configuration, the nano objects parameters, the 3D navigation window and so on...

It is a best practice to set an higher heap memory size in the Java Virtual Machine configuration, e.g.: -Xmx5000M -Xms5000M

Some of the simulation parameters have to be defined in the command line and depend on the type of simulation chosen, e.g.: -simBlood or -simTCPLike.

for the MolComML configuration file: -simMolComML (Please note that the actual version of the MolComML importer is compatible only with the Diffusion Based scenario, described by the configuration file "punctiformEmitter_xml_revised_2.3.xml" provided in the above package "BiNS2_v.17.6 MolComML integration")

You may want to change these values according to your simulation needs. For a detailed explanation of these parameters, refer to our publications. A more detailed guide will be soon published here.

Run

To execute the simulation launch java -jar bins2_v.14.3.jar followed by the simulation parameters defined at points 2 and 3 on the configuration section.